Publication: Proteomic profiling of developing cotton fibers using iTRAQ
Hu and colleagues from Professor Jonathan Wendel’s laboratory at Iowa State University used the 8-plex iTRAQ-based quantitative Proteomics workflow to investigate the development and evolution of cotton fibers from the wild and domesticated Gossypium barbadense. The 1317 identified fiber proteins provide a rich database for functional analyses of cotton improvement or evolution. Proteomics division director Sixue Chen and post doctoral student Jin Koh contributed to these findings.
Pima cotton (Gossypium barbadense) is widely cultivated because of its long, strong seed
trichomes (‘fibers’) used for premium textiles. These agronomically advanced fibers were
derived following domestication and thousands of years of human-mediated crop improvement.
To gain an insight into fiber development and evolution, we conducted comparative
proteomic and transcriptomic profiling of developing fiber from an elite cultivar and a wild
Analyses using isobaric tag for relative and absolute quantification (iTRAQ) LC-MS/MS
technology identified 1317 proteins in fiber. Of these, 205 were differentially expressed
across developmental stages, and 190 showed differential expression between wild and cultivated
forms, 14.4% of the proteome sampled. Human selection may have shifted the timing
of developmental modules, such that some occur earlier in domesticated than in wild cotton.
A novel approach was used to detect possible biased expression of homoeologous copies of
proteins. Results indicate a significant partitioning of duplicate gene expression at the protein
level, but an approximately equal degree of bias for each of the two constituent genomes of
Our results demonstrate the power of complementary transcriptomic and proteomic
approaches for the study of the domestication process. They also provide a rich database for
mining for functional analyses of cotton improvement or evolution.